Supplementary Table 1 - List of XLID cases analyzed in this study
Case# / Array / Gender / Family / Known Mutations / Sanger sequencing
ID1 / AVG_Signal.1825371092_E / M
ID2 / AVG_Signal.1699538165_E / M
ID3 / AVG_Signal.1699538165_C / M
ID4 / AVG_Signal.1699538165_G / M
ID5 / AVG_Signal.1825371092_D / M / JARID1C / SS
ID6 / AVG_Signal.1825371054_G / M
ID7 / AVG_Signal.1699538165_F / M
ID8 / AVG_Signal.1825371092_G / M
ID9 / AVG_Signal.1825371092_C / M
ID10 / AVG_Signal.1740115075_G / M
ID11 / AVG_Signal.1825371092_F / M / CCDC22 mutation identified in this study / SS
ID12 / AVG_Signal.1699538152_B / M
ID13 / AVG_Signal.1825371054_D / M / PQBP1-F1(ID13,ID14,ID15). ID13-unaffected father
ID14 / AVG_Signal.1825371054_C / M / PQBP1-F1(ID13,ID14,ID15). ID13-unaffected father
ID15 / AVG_Signal.1825371054_H / M / PQBP1-F1(ID13,ID14,ID15). ID13-unaffected father
ID16 / AVG_Signal.1825371082_A / M / ID16,ID17
ID17 / AVG_Signal.1825371082_B / M / ID16,ID17
ID18 / AVG_Signal.1825371092_B / M / ND / SS
ID19 / AVG_Signal.1699538152_D / M / HUWE1 duplication
ID20 / AVG_Signal.1825371093_E / M / ID20,ID21
ID21 / AVG_Signal.1825371093_F / M / ID20,ID21
ID22 / AVG_Signal.1699538165_D / M
ID23 / AVG_Signal.1825371093_A / M
ID24 / AVG_Signal.1740115075_H / M
ID25 / AVG_Signal.1825371082_E / M / CASK / SS
ID26 / AVG_Signal.1825371092_H / M
ID27 / AVG_Signal.1740115074_H / M / ND / SS
ID28 / AVG_Signal.1825371082_D / M
ID29 / AVG_Signal.1740115075_B / M
ID30 / AVG_Signal.1740115074_D / M
ID31 / AVG_Signal.1825371092_A / M / ND / SS
ID32 / AVG_Signal.1740115074_B / M
ID33 / AVG_Signal.1740115074_C / M
ID34 / AVG_Signal.1699538152_C / M / ND, CCDC22 c.715G>A, p.E239K / SS
ID35 / AVG_Signal.1740115074_E / M / ND / SS
ID36 / AVG_Signal.1699538165_A / M / ND / SS
ID37 / AVG_Signal.1740115075_C / M
ID38 / AVG_Signal.1740115075_D / M / ND / SS
ID39 / AVG_Signal.1699538152_F / M
ID40 / AVG_Signal.1740115074_A / M
ID41 / AVG_Signal.1740115075_A / M / HUWE1 dup
ID42 / AVG_Signal.1825371093_B / M
ID43 / AVG_Signal.1825371093_C / M / ND / SS
ID44 / AVG_Signal.1699538152_H / M
ID45 / AVG_Signal.1740115075_E / M / IL1RAPL1 insA / SS
ID46 / AVG_Signal.1825371082_F / M
ID47 / AVG_Signal.1699538165_B / M
ID48 / AVG_Signal.1699538165_H / M / ND / SS
ID49 / AVG_Signal.1699538152_G / M / ID49,ID50
ID49 / AVG_Signal.1825371082_H / M / ID49,ID50 / TR
ID50 / AVG_Signal.1740115074_G / M / ID49,ID50
ID51 / AVG_Signal.1825371082_G / M / PHF6
The table lists all ID cases for which the RNA and microarray data passed the quality control criteria. The array name identifies the corresponding expression data in the raw data file. For cases where more than one family member was included in the study, all family members are listed in the fourth column. SS- Proband Sanger sequenced by Tarpey et al (ref#5), ND- No obvious disease-causing variant identified yet by Sanger sequencing, TR- technical replicate.
Supplementary Table 2. Phenotype characterization of PQBP1 mutations described in this study
Family/Case / Phenotype
PQBP1-F1a (ID14,ID15) / Moderate mental retardation (3/3), normal head circumference (3/3), short stature (2/3), submucous cleft palate (1/3), velopharyngeal incompetence (1/3), hypospadias and unilateral renal agenesis (1/3). Facial features (3/3): high nasal bridge, arched eyebrows, upslanting palpebral fissures, hypertelorism, long palpebral fissures, short philtrum, small mouth and narrow chin.
ID30 / Mild to moderate mental retardation, short stature, microcephaly and brachycephaly with a sloping forehead, slightly upslanting palpebral fissures, high nasal bridge and bulbous nasal tip, prominent ears, long fingers and short bulbous great toes.
a- The PQBP1-F1 family consists of three affected brothers, two of which were included in the expression profiling data set (ID14, ID15). All three brothers carry the (AG)2 deletion. The frequency of specific clinical features is given between brackets
Supplementary Table 3. Primers for CCDC22 and PQBP1
Primer Name / F/R / Sequence / Size (bp) / Location / Product Sizes
CCDC22 gDNA sequencing
P-I / F / CAGCAGCTATTGCAAGCTCAAC / 22 / Promoter / 373 bp
R / GAGCCCTGAATGTCAGGATC / 20 / Intron 1
CCDC22 RT-qPCR
E1-E4 / F / ACTTTCCAACTCTCCCCACAC / 21 / 5’UTR / 515 bp
R / CCGGAGGAGAATAGCTGAGT / 20 / Exon 4
Long I1-E3 / F / CACATCCGGGACTCTAAAGC / 20 / Intron 1a / 1 646 bpb
R / AGACGCTCAGCCAAGAAGAG / 20 / Exon 3
E1-E2 / F / GGACCGAATCCTCATCCATTC / 21 / Exon 1 / 103 bp
R / ACAGCCTCTACAACCAGCTCA / 21 / Exon 2
I1-E3 / F / ATCAAGCTGGTCCCCTTCTT / 20 / Intron 1c / 229 bpd
R / AGCCAAGCTCCAAGGGATAG / 20 / Exon 3
E1 / F / ACTTTCCAACTCTCCCCACAC / 21 / 5’UTR / 167 bp
R / CAGCGAATGGATGAGGATTC / 20 / Exon 1
E17 / F / CTCGAGGAGCAGATCGAGAC / 20 / Exon 17 / 105 bp
R / TAGGAGGCCAGCGTTCTCC / 19 / Exon 17
PQBP1 RT-qPCR
PQBP1-F / F / GAGAGAGCGAGACAGGGAAC
PQBP1-R / R / TTTCGGCTTACTGCCTTCTT
a 33 bp apart from exon 1; b 6 397bp if amplified from gDNA; c 3 bp apart from exon 2; d 4 980 bp if
amplified from gDNA. F, forward primer; R, reverse primer

Supplementary Figure 1


Supplementary Figure 2

Supplementary Figure 3.


SUPPLEMENTARY METHODS

Patients

All of the cases used in this study (Supplementary Table 1) have been diagnosed with intellectual disability and had a pedigree consistent with X-linked inheritance. The majority of cases were probands from unrelated families. In addition, four families with more than one affected member were included in the study. A few cases had known causal mutations (Supplementary Table 1) none of which caused mRNA downregulation of the mutated gene.

The controls used in this study were unaffected siblings of autism patients from the AGRE cohort (http://research.agre.org/). Genome-wide expression profiles from controls LCLs were obtained as part of an independent study.

Microarrays

Total RNA was extracted from LCLs using the Qiagen miRNeasy kit, and RNA quality was assessed by Agilent Bioanalyzer. Genome-wide expression profiles were obtained on Illumina Ref8 v2 microarrays (XLID cases) and Illumina Ref8 v3 microarrays (controls). cDNA labeling and array hybridizations were performed following the manufacturer’s protocol at the UCLA microarray core facility (http://microarray.genetics.ucla.edu/xowiki/).

Microarray data analysis was performed using the R software and the Bioconductor “Lumi” package(1). Raw data was log2 transformed and normalized by quantile normalization. Batch effects were adjusted using the ComBat package(2). Microarray data quality control criteria included high inter-array Pearson correlation coefficients (PCC>0.9), low variance of mean inter-array correlation and probe detection P values <0.05 in at least 50% on the samples. 52 of the 64 RNA samples analyzed passed all the RNA and data quality control criteria and were retained for further analysis (Supplementary Table 1).

Genes with expression levels outside the 99.7% confidence interval (3 standard deviations below the mean) in a single case, or outside the 95% confidence interval (2 standard deviations below the mean) in two cases from the same family were considered significantly downregulated and followed up by RT-qPCR.

RT-PCR and RT-qPCR

Total RNA for RT-PCR and RT-qPCR was extracted from LCLs with Trizol Reagent (Invitrogen) combined with RNeasy mini kit (Qiagen) and treated with DNase I (Qiagen). 2 μg of RNA with 1 μg of random hexanucleotide primers (Invitrogen) were annealed at 65oC and then incubated on ice for at least 2 minutes. Reverse transcriptional reagents (Invitrogen, SuperScript III Reverse Transcriptase Kit) are incubated at 25°C for 5mins and then 50° C for 60 mins Superscript III (Invitrogen). The efficiency of the reaction was tested by PCR using primers specific to the ubiquitously expressed ACTB gene. cDNAs were amplified with Taq DNA polymerase (Roche) and specific single-stranded DNA primers (35 cycles of denaturation, 94°C for 30 s; annealing for 30 s (specific Tm for each pair of primers, see Supplementary Table 2); extension, 72 °C for 30 s, ). PCR products were analyzed by 1% agarose gel stained with Ethidium Bromide. Real-time PCR was performed using StepOnePlus Real-time PCR system (Applied Biosystems, Foster City, CA.). RT-qPCR reactions were performed in 20 microliters volume containing iTaq Sybrgreen (Biorad) and primers at a concentration of 0.5μM each. Primers used in RT-PCR and RT-qPCR were designed by Primer 3 and specificity was checked by NCBI BLAST (Supplementary Table 2).

CHX Treatment

Approximately 3×106 cells were incubated in RPMI with 10% FCS and 100 μg ml−1 cycloheximide (Sigma) for 6 hrs. All samples were treated in triplicate. Before RNA extraction the cells were harvested by centrifugation and washed in PBS(3).

Statistical Analysis

P value was calculated using Student’s paired, two-tailed t-test when comparing the difference between CHX treatment groups. When comparing the difference between controls and patients, P value was calculated using Student’s unpaired, two-tailed t-test.

Western Blot

LCL cell pellets were lysed in ice-cold radioimmunoprecipitation assay (RIPA) buffer (50 mM Tris pH 8.0, 150 mM NaCl, 1% Nonidet P-40, 0.5% sodium deoxycholate, 0.1% SDS and protease inhibitors) and incubated on ice for 30 min. Debris was removed by high-speed centrifugation for 10 min at 4°C. Cleared lysates were quantitated by Bradford Assay (Bio-Rad). Approximately equal quantity of proteins were separated on a NuPAGE Novex 4-12% Bis-Tris Gel (Invitrogen, 1.0 mm, 12 wells. Cat.No.NP0322BOX) and then transferred onto nitrocellulose membranes by semidry electroblotting using a Trans-Blot SD Semi-Dry Transfer Cell (Bio-Rad). Membranes were blocked with 5% skim milk and 1% goat serum and then incubated with appropriate primary antibody (Sigma-Aldrich Anti-CCDC22 antibody, HPA000888) and subsequently with secondary HRP-conjugated antibody (Goat anti-Rabbit HRP-conjugated antibody). The blots were developed using the enhanced chemiluminescence (ECL) method (Amersham). Densitometry was performed on low-exposured film to determine the protein level using GeneTools analysis software (Syngene software).

mTOM The mTOM analysis was performed using the available software (http://www.genetics.ucla.edu/labs/horvath/MTOM/) with the cortex expression data from Johnson et al.(4) as input. The default soft-threshold power of 6 was used for calculating the adjacency matrix, and the “signed” option was used in order to take into account the directionality of expression changes. The multi-node topological overlap module was built in a non-recursive manner, to limit the detection of co-expressed genes to those most specific to CCDC22.

Gene ontology analysis was performed using the online DAVID tool (http://david.abcc.ncifcrf.gov/) The p values reported are corrected for multiple comparisons (Benjamini and Hochberg).

1. Du P, Kibbe WA, Lin SM. Bioinformatics 2008 Jul 1; 24(13): 1547-1548.

2. Johnson WE, Li C, Rabinovic A. Biostatistics 2007 Jan; 8(1): 118-127.

3. Tarpey PS, Raymond FL, Nguyen LS, Rodriguez J, Hackett A, Vandeleur L et al. Nat Genet 2007 Sep; 39(9): 1127-1133.

4. Johnson MB, Kawasawa YI, Mason CE, Krsnik Z, Coppola G, Bogdanovic D et al. Neuron 2009 May 28; 62(4): 494-509.